Multiple sequence alignment - TraesCS2A01G087900

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G087900 chr2A 100.000 2597 0 0 1 2597 41226652 41229248 0.000000e+00 4796.0
1 TraesCS2A01G087900 chr2A 92.222 810 58 5 1 807 41213652 41214459 0.000000e+00 1142.0
2 TraesCS2A01G087900 chr2A 98.681 455 6 0 811 1265 41217787 41218241 0.000000e+00 808.0
3 TraesCS2A01G087900 chr2A 91.244 434 24 8 839 1265 41207960 41208386 1.730000e-161 579.0
4 TraesCS2A01G087900 chr2A 79.647 624 98 18 1056 1655 41170291 41170909 3.090000e-114 422.0
5 TraesCS2A01G087900 chr2A 85.496 393 50 4 1270 1659 41218321 41218709 1.120000e-108 403.0
6 TraesCS2A01G087900 chr2A 85.242 393 51 4 1270 1659 41208466 41208854 5.210000e-107 398.0
7 TraesCS2A01G087900 chr2A 81.985 272 45 3 471 738 41207270 41207541 7.230000e-56 228.0
8 TraesCS2A01G087900 chr2D 94.360 727 36 3 3 728 36787093 36787815 0.000000e+00 1110.0
9 TraesCS2A01G087900 chr2D 90.585 393 28 4 897 1285 36783349 36783736 1.780000e-141 512.0
10 TraesCS2A01G087900 chr2D 79.645 619 91 16 1058 1659 36779557 36780157 1.860000e-111 412.0
11 TraesCS2A01G087900 chr2D 85.185 378 47 6 1283 1656 36783821 36784193 1.890000e-101 379.0
12 TraesCS2A01G087900 chr2D 85.612 139 17 3 2005 2141 18981594 18981457 2.690000e-30 143.0
13 TraesCS2A01G087900 chr2D 84.892 139 18 3 2005 2141 18877839 18877702 1.250000e-28 137.0
14 TraesCS2A01G087900 chr2B 89.120 818 70 12 1 806 63246780 63247590 0.000000e+00 1000.0
15 TraesCS2A01G087900 chr2B 89.837 738 63 9 48 782 63253791 63254519 0.000000e+00 937.0
16 TraesCS2A01G087900 chr2B 90.061 654 32 16 1057 1683 63260768 63261415 0.000000e+00 817.0
17 TraesCS2A01G087900 chr2B 91.264 435 22 4 839 1265 63220835 63221261 1.730000e-161 579.0
18 TraesCS2A01G087900 chr2B 92.424 396 20 4 875 1265 63249838 63250228 8.120000e-155 556.0
19 TraesCS2A01G087900 chr2B 90.952 420 25 4 875 1285 63255074 63255489 1.050000e-153 553.0
20 TraesCS2A01G087900 chr2B 79.180 634 103 20 1059 1677 63140690 63141309 1.860000e-111 412.0
21 TraesCS2A01G087900 chr2B 95.312 256 11 1 811 1066 63260068 63260322 3.110000e-109 405.0
22 TraesCS2A01G087900 chr2B 83.632 391 51 7 1275 1659 63255539 63255922 3.180000e-94 355.0
23 TraesCS2A01G087900 chr2B 93.143 175 11 1 1 175 63253613 63253786 3.320000e-64 255.0
24 TraesCS2A01G087900 chr2B 84.530 181 21 1 120 293 63219526 63219706 3.440000e-39 172.0
25 TraesCS2A01G087900 chr7D 93.310 583 38 1 2016 2597 506717776 506718358 0.000000e+00 859.0
26 TraesCS2A01G087900 chr7D 90.909 77 7 0 1983 2059 506717713 506717789 1.270000e-18 104.0
27 TraesCS2A01G087900 chr6B 77.358 689 109 28 1936 2590 610086001 610086676 5.280000e-97 364.0
28 TraesCS2A01G087900 chr5A 81.333 450 44 13 1927 2337 546358901 546358453 1.930000e-86 329.0
29 TraesCS2A01G087900 chr5D 71.897 701 150 28 1925 2592 120897780 120898466 2.670000e-35 159.0
30 TraesCS2A01G087900 chr7B 71.367 695 155 32 1925 2597 455758568 455757896 9.690000e-30 141.0
31 TraesCS2A01G087900 chr1D 87.500 88 9 2 188 275 46493216 46493131 1.640000e-17 100.0
32 TraesCS2A01G087900 chr4D 84.946 93 9 3 235 324 490261490 490261400 3.560000e-14 89.8
33 TraesCS2A01G087900 chr1A 85.227 88 11 2 188 275 46262526 46262441 3.560000e-14 89.8
34 TraesCS2A01G087900 chr4A 86.885 61 7 1 172 232 468575927 468575868 1.670000e-07 67.6
35 TraesCS2A01G087900 chr7A 96.875 32 1 0 1923 1954 250693341 250693310 1.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G087900 chr2A 41226652 41229248 2596 False 4796.000000 4796 100.000000 1 2597 1 chr2A.!!$F2 2596
1 TraesCS2A01G087900 chr2A 41213652 41218709 5057 False 784.333333 1142 92.133000 1 1659 3 chr2A.!!$F4 1658
2 TraesCS2A01G087900 chr2A 41170291 41170909 618 False 422.000000 422 79.647000 1056 1655 1 chr2A.!!$F1 599
3 TraesCS2A01G087900 chr2A 41207270 41208854 1584 False 401.666667 579 86.157000 471 1659 3 chr2A.!!$F3 1188
4 TraesCS2A01G087900 chr2D 36779557 36787815 8258 False 603.250000 1110 87.443750 3 1659 4 chr2D.!!$F1 1656
5 TraesCS2A01G087900 chr2B 63260068 63261415 1347 False 611.000000 817 92.686500 811 1683 2 chr2B.!!$F4 872
6 TraesCS2A01G087900 chr2B 63246780 63255922 9142 False 609.333333 1000 89.851333 1 1659 6 chr2B.!!$F3 1658
7 TraesCS2A01G087900 chr2B 63140690 63141309 619 False 412.000000 412 79.180000 1059 1677 1 chr2B.!!$F1 618
8 TraesCS2A01G087900 chr2B 63219526 63221261 1735 False 375.500000 579 87.897000 120 1265 2 chr2B.!!$F2 1145
9 TraesCS2A01G087900 chr7D 506717713 506718358 645 False 481.500000 859 92.109500 1983 2597 2 chr7D.!!$F1 614
10 TraesCS2A01G087900 chr6B 610086001 610086676 675 False 364.000000 364 77.358000 1936 2590 1 chr6B.!!$F1 654

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
782 3602 0.038618 CCACTCCGATGACAACGACA 60.039 55.0 6.69 0.0 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 18239 0.031616 TGGCCACAAAAAGAAGGGGT 60.032 50.0 0.0 0.0 0.0 4.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 2604 9.635404 GGGATATACAACTAGCTAGTGAGATAT 57.365 37.037 26.70 24.07 36.50 1.63
167 2688 5.179368 ACACTCGGACATGAACAGTAAATTG 59.821 40.000 0.00 0.00 0.00 2.32
211 2741 2.440627 AGGCATCCAAGATGCTCATGTA 59.559 45.455 24.33 0.00 44.02 2.29
329 3046 0.690192 TGAAGCCGATGTTTCCTCCA 59.310 50.000 0.00 0.00 31.28 3.86
330 3047 1.281867 TGAAGCCGATGTTTCCTCCAT 59.718 47.619 0.00 0.00 31.28 3.41
405 3129 0.753262 ATCTAGCGTGGCAAGGTAGG 59.247 55.000 29.89 16.85 39.41 3.18
472 3281 0.969409 GGTAGCGTGTAGGGAGTGGT 60.969 60.000 0.00 0.00 0.00 4.16
514 3323 2.972505 CGTTGTCGTGCTGGCCTT 60.973 61.111 3.32 0.00 0.00 4.35
548 3357 1.134220 GCCTGGGTCCACGATTAATCA 60.134 52.381 15.57 0.00 0.00 2.57
563 3373 2.185310 AATCAGGACCACCACGGAGC 62.185 60.000 0.00 0.00 38.63 4.70
593 3403 4.314440 GACAGTGCCGCCTGGACA 62.314 66.667 0.00 0.00 36.75 4.02
643 3454 0.315251 CTCAACGACACCTCTGCTGA 59.685 55.000 0.00 0.00 0.00 4.26
782 3602 0.038618 CCACTCCGATGACAACGACA 60.039 55.000 6.69 0.00 0.00 4.35
784 3604 2.337583 CACTCCGATGACAACGACAAT 58.662 47.619 6.69 0.00 0.00 2.71
789 3609 2.672874 CCGATGACAACGACAATGACAT 59.327 45.455 6.69 0.00 36.22 3.06
791 3611 3.484065 CGATGACAACGACAATGACATGG 60.484 47.826 0.00 0.00 34.24 3.66
1370 15205 2.260434 GAAGTGGCCGTCGCACTA 59.740 61.111 6.02 0.00 36.38 2.74
1372 15207 3.584868 AAGTGGCCGTCGCACTACC 62.585 63.158 6.02 0.00 36.38 3.18
1397 15232 3.500642 GAGCGCCTCGGCCTTTTC 61.501 66.667 2.29 0.00 37.98 2.29
1401 15236 2.438614 GCCTCGGCCTTTTCCTCC 60.439 66.667 0.00 0.00 34.56 4.30
1504 15339 4.947147 GGTGCAAGGTCACCGCCA 62.947 66.667 0.00 0.00 45.95 5.69
1507 15342 2.359850 GCAAGGTCACCGCCATCA 60.360 61.111 0.00 0.00 0.00 3.07
1508 15343 1.971167 GCAAGGTCACCGCCATCAA 60.971 57.895 0.00 0.00 0.00 2.57
1509 15344 1.926511 GCAAGGTCACCGCCATCAAG 61.927 60.000 0.00 0.00 0.00 3.02
1513 15348 2.747460 TCACCGCCATCAAGCAGC 60.747 61.111 0.00 0.00 0.00 5.25
1517 15358 3.869272 CGCCATCAAGCAGCGGTC 61.869 66.667 0.00 0.00 45.88 4.79
1518 15359 3.512516 GCCATCAAGCAGCGGTCC 61.513 66.667 0.00 0.00 0.00 4.46
1659 15519 5.337773 GGACAAAATTGTTACGCGTTTACTC 59.662 40.000 20.78 7.80 42.43 2.59
1660 15520 4.899616 ACAAAATTGTTACGCGTTTACTCG 59.100 37.500 20.78 0.55 38.47 4.18
1661 15521 4.970472 AAATTGTTACGCGTTTACTCGA 57.030 36.364 20.78 7.41 0.00 4.04
1662 15522 4.557276 AATTGTTACGCGTTTACTCGAG 57.443 40.909 20.78 11.84 36.75 4.04
1664 15524 3.804518 TGTTACGCGTTTACTCGAGTA 57.195 42.857 20.78 21.25 42.82 2.59
1665 15525 3.479006 TGTTACGCGTTTACTCGAGTAC 58.521 45.455 24.60 15.93 43.17 2.73
1666 15526 3.186409 TGTTACGCGTTTACTCGAGTACT 59.814 43.478 24.60 1.59 43.17 2.73
1667 15527 2.238245 ACGCGTTTACTCGAGTACTG 57.762 50.000 24.60 17.08 41.39 2.74
1669 15529 2.736721 ACGCGTTTACTCGAGTACTGTA 59.263 45.455 24.60 7.70 41.39 2.74
1670 15530 3.087124 CGCGTTTACTCGAGTACTGTAC 58.913 50.000 24.60 17.35 0.00 2.90
1671 15531 3.181526 CGCGTTTACTCGAGTACTGTACT 60.182 47.826 24.60 19.79 42.86 2.73
1672 15532 4.667668 CGCGTTTACTCGAGTACTGTACTT 60.668 45.833 24.60 8.30 39.59 2.24
1673 15533 4.552660 GCGTTTACTCGAGTACTGTACTTG 59.447 45.833 24.60 23.52 39.59 3.16
1676 15536 6.634436 CGTTTACTCGAGTACTGTACTTGTTT 59.366 38.462 24.60 19.17 40.40 2.83
1678 15538 8.896826 GTTTACTCGAGTACTGTACTTGTTTAC 58.103 37.037 24.60 17.31 40.40 2.01
1681 15541 6.423905 ACTCGAGTACTGTACTTGTTTACGTA 59.576 38.462 26.57 11.05 40.40 3.57
1684 15544 9.098355 TCGAGTACTGTACTTGTTTACGTATAT 57.902 33.333 26.57 1.57 40.40 0.86
1715 18079 7.934665 AGTGTATTACTTGTTTCATGTGTACCA 59.065 33.333 0.00 0.00 35.67 3.25
1721 18085 5.065988 ACTTGTTTCATGTGTACCAGTGTTC 59.934 40.000 0.00 0.00 0.00 3.18
1723 18087 2.448926 TCATGTGTACCAGTGTTCCG 57.551 50.000 0.00 0.00 0.00 4.30
1736 18124 5.183140 ACCAGTGTTCCGGAGAAAAATATTG 59.817 40.000 3.34 0.00 32.58 1.90
1737 18125 5.095490 CAGTGTTCCGGAGAAAAATATTGC 58.905 41.667 3.34 0.00 32.58 3.56
1738 18126 4.764823 AGTGTTCCGGAGAAAAATATTGCA 59.235 37.500 3.34 0.00 32.58 4.08
1739 18127 5.095490 GTGTTCCGGAGAAAAATATTGCAG 58.905 41.667 3.34 0.00 32.58 4.41
1740 18128 4.764823 TGTTCCGGAGAAAAATATTGCAGT 59.235 37.500 3.34 0.00 32.58 4.40
1741 18129 5.941058 TGTTCCGGAGAAAAATATTGCAGTA 59.059 36.000 3.34 0.00 32.58 2.74
1743 18131 6.618287 TCCGGAGAAAAATATTGCAGTATG 57.382 37.500 0.00 0.00 40.87 2.39
1768 18156 9.988815 TGCTTTTACTTTAAATTATTGCTTCCA 57.011 25.926 0.00 0.00 0.00 3.53
1804 18192 9.397280 AGATTAAATAGAGTAAGGAAGCAAACC 57.603 33.333 0.00 0.00 0.00 3.27
1807 18195 3.425162 AGAGTAAGGAAGCAAACCCAG 57.575 47.619 0.00 0.00 0.00 4.45
1808 18196 1.813178 GAGTAAGGAAGCAAACCCAGC 59.187 52.381 0.00 0.00 0.00 4.85
1810 18198 0.777446 TAAGGAAGCAAACCCAGCCT 59.223 50.000 0.00 0.00 0.00 4.58
1811 18199 0.540597 AAGGAAGCAAACCCAGCCTC 60.541 55.000 0.00 0.00 0.00 4.70
1812 18200 1.075659 GGAAGCAAACCCAGCCTCT 59.924 57.895 0.00 0.00 0.00 3.69
1815 18203 2.087646 GAAGCAAACCCAGCCTCTTAG 58.912 52.381 0.00 0.00 0.00 2.18
1816 18204 1.068121 AGCAAACCCAGCCTCTTAGT 58.932 50.000 0.00 0.00 0.00 2.24
1817 18205 1.003696 AGCAAACCCAGCCTCTTAGTC 59.996 52.381 0.00 0.00 0.00 2.59
1819 18207 2.427506 CAAACCCAGCCTCTTAGTCAC 58.572 52.381 0.00 0.00 0.00 3.67
1820 18208 2.031495 AACCCAGCCTCTTAGTCACT 57.969 50.000 0.00 0.00 0.00 3.41
1821 18209 2.031495 ACCCAGCCTCTTAGTCACTT 57.969 50.000 0.00 0.00 0.00 3.16
1823 18211 1.065854 CCCAGCCTCTTAGTCACTTGG 60.066 57.143 0.00 0.00 0.00 3.61
1824 18212 1.625818 CCAGCCTCTTAGTCACTTGGT 59.374 52.381 0.00 0.00 0.00 3.67
1825 18213 2.354203 CCAGCCTCTTAGTCACTTGGTC 60.354 54.545 0.00 0.00 0.00 4.02
1826 18214 1.903183 AGCCTCTTAGTCACTTGGTCC 59.097 52.381 0.00 0.00 0.00 4.46
1827 18215 1.404315 GCCTCTTAGTCACTTGGTCCG 60.404 57.143 0.00 0.00 0.00 4.79
1828 18216 2.168496 CCTCTTAGTCACTTGGTCCGA 58.832 52.381 0.00 0.00 0.00 4.55
1829 18217 2.094649 CCTCTTAGTCACTTGGTCCGAC 60.095 54.545 0.00 0.00 0.00 4.79
1830 18218 1.891150 TCTTAGTCACTTGGTCCGACC 59.109 52.381 10.96 10.96 39.22 4.79
1838 18226 3.650023 TGGTCCGACCAGTGGTTT 58.350 55.556 17.93 0.00 44.79 3.27
1839 18227 2.837411 TGGTCCGACCAGTGGTTTA 58.163 52.632 17.93 1.90 44.79 2.01
1841 18229 0.393820 GGTCCGACCAGTGGTTTACA 59.606 55.000 17.93 0.00 38.42 2.41
1842 18230 1.202675 GGTCCGACCAGTGGTTTACAA 60.203 52.381 17.93 0.00 38.42 2.41
1843 18231 2.140717 GTCCGACCAGTGGTTTACAAG 58.859 52.381 17.93 4.27 35.25 3.16
1844 18232 2.040939 TCCGACCAGTGGTTTACAAGA 58.959 47.619 17.93 4.64 35.25 3.02
1845 18233 2.435069 TCCGACCAGTGGTTTACAAGAA 59.565 45.455 17.93 0.00 35.25 2.52
1846 18234 3.118334 TCCGACCAGTGGTTTACAAGAAA 60.118 43.478 17.93 0.00 35.25 2.52
1847 18235 3.628487 CCGACCAGTGGTTTACAAGAAAA 59.372 43.478 17.93 0.00 35.25 2.29
1848 18236 4.096682 CCGACCAGTGGTTTACAAGAAAAA 59.903 41.667 17.93 0.00 35.25 1.94
1849 18237 5.270853 CGACCAGTGGTTTACAAGAAAAAG 58.729 41.667 17.93 0.00 35.25 2.27
1851 18239 5.265989 ACCAGTGGTTTACAAGAAAAAGGA 58.734 37.500 9.70 0.00 27.29 3.36
1852 18240 5.126545 ACCAGTGGTTTACAAGAAAAAGGAC 59.873 40.000 9.70 0.00 27.29 3.85
1855 18243 3.962063 TGGTTTACAAGAAAAAGGACCCC 59.038 43.478 0.00 0.00 0.00 4.95
1856 18244 4.220724 GGTTTACAAGAAAAAGGACCCCT 58.779 43.478 0.00 0.00 33.87 4.79
1859 18247 3.973472 ACAAGAAAAAGGACCCCTTCT 57.027 42.857 0.00 0.00 43.92 2.85
1860 18248 4.265856 ACAAGAAAAAGGACCCCTTCTT 57.734 40.909 7.07 7.07 43.92 2.52
1861 18249 4.620723 ACAAGAAAAAGGACCCCTTCTTT 58.379 39.130 9.34 3.00 43.92 2.52
1864 18252 5.614324 AGAAAAAGGACCCCTTCTTTTTG 57.386 39.130 15.52 0.00 46.64 2.44
1865 18253 5.030147 AGAAAAAGGACCCCTTCTTTTTGT 58.970 37.500 15.52 10.49 46.64 2.83
1866 18254 4.753516 AAAAGGACCCCTTCTTTTTGTG 57.246 40.909 0.00 0.00 43.92 3.33
1867 18255 2.381752 AGGACCCCTTCTTTTTGTGG 57.618 50.000 0.00 0.00 0.00 4.17
1872 18413 0.681175 CCCTTCTTTTTGTGGCCAGG 59.319 55.000 5.11 0.00 0.00 4.45
1873 18414 0.033920 CCTTCTTTTTGTGGCCAGGC 59.966 55.000 5.11 1.26 0.00 4.85
1875 18416 2.356194 CTTTTTGTGGCCAGGCGC 60.356 61.111 5.11 0.00 0.00 6.53
1898 18439 2.372074 GGATCCGGCACCCCTACAA 61.372 63.158 0.00 0.00 0.00 2.41
1900 18441 0.463833 GATCCGGCACCCCTACAAAG 60.464 60.000 0.00 0.00 0.00 2.77
1902 18443 1.074248 CCGGCACCCCTACAAAGTT 59.926 57.895 0.00 0.00 0.00 2.66
1949 18490 7.078011 GATCTTTTTAAAAGATCTGTCGCCT 57.922 36.000 34.82 15.34 45.62 5.52
1967 18509 1.268794 CCTAGCGAGTCGTTGATCTGG 60.269 57.143 15.08 4.05 0.00 3.86
1968 18510 1.402259 CTAGCGAGTCGTTGATCTGGT 59.598 52.381 15.08 0.00 0.00 4.00
1969 18511 0.109086 AGCGAGTCGTTGATCTGGTG 60.109 55.000 15.08 0.00 0.00 4.17
1970 18512 0.109272 GCGAGTCGTTGATCTGGTGA 60.109 55.000 15.08 0.00 0.00 4.02
1977 18519 2.028203 TCGTTGATCTGGTGATTGAGCA 60.028 45.455 0.00 0.00 32.19 4.26
1996 18538 2.616458 GCCTGGGGTCACCTTCCAT 61.616 63.158 0.00 0.00 41.11 3.41
2003 18545 1.341383 GGGTCACCTTCCATCATTGCT 60.341 52.381 0.00 0.00 0.00 3.91
2014 18556 2.286595 CCATCATTGCTACACATGTCGC 60.287 50.000 0.00 0.00 37.27 5.19
2108 18680 5.821516 TCTTGTAACGGATGTTTTGTTGT 57.178 34.783 0.00 0.00 39.54 3.32
2298 19009 2.306255 GATGGTGGGCGACGGTGTAT 62.306 60.000 0.00 0.00 0.00 2.29
2307 19168 1.517832 GACGGTGTATGCAGCTCCT 59.482 57.895 11.25 0.00 40.67 3.69
2445 19307 2.260434 GACCTTGTCGGCGTGCTA 59.740 61.111 6.85 0.00 35.61 3.49
2488 19380 0.238553 GCGAGAAGGAGTTGGTTTGC 59.761 55.000 0.00 0.00 0.00 3.68
2514 19406 1.216710 CTTGGGAGGAGCACGAGTC 59.783 63.158 0.00 0.00 0.00 3.36
2515 19407 1.533033 TTGGGAGGAGCACGAGTCA 60.533 57.895 0.00 0.00 0.00 3.41
2541 19433 0.978146 CTCTCGTGGGGGTCCAGATT 60.978 60.000 0.00 0.00 45.05 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
127 2648 5.655090 TCCGAGTGTAAATGAGGTCATCTTA 59.345 40.000 0.00 0.00 35.10 2.10
211 2741 2.818130 AATTTGCATGAACCTTGCGT 57.182 40.000 0.00 0.00 43.10 5.24
329 3046 1.145759 CGTCCGATACGCAGTTGCAT 61.146 55.000 4.84 0.00 46.10 3.96
330 3047 1.803922 CGTCCGATACGCAGTTGCA 60.804 57.895 4.84 0.00 46.10 4.08
589 3399 4.200283 CCGGCGAGCTCTCTGTCC 62.200 72.222 9.30 4.19 0.00 4.02
593 3403 2.909965 GATCCCGGCGAGCTCTCT 60.910 66.667 9.30 0.00 0.00 3.10
682 3495 4.641645 CTGCCTCGGCCAACACCA 62.642 66.667 2.24 0.00 41.09 4.17
782 3602 1.809619 CGTCGTCGGCCATGTCATT 60.810 57.895 2.24 0.00 0.00 2.57
807 4778 0.676736 CCTCTGGGTAGAATCGGCTC 59.323 60.000 0.00 0.00 31.21 4.70
808 4779 1.403687 GCCTCTGGGTAGAATCGGCT 61.404 60.000 0.00 0.00 38.25 5.52
809 4780 1.069935 GCCTCTGGGTAGAATCGGC 59.930 63.158 0.00 0.00 35.46 5.54
812 8854 0.676736 CTCCGCCTCTGGGTAGAATC 59.323 60.000 0.00 0.00 31.21 2.52
1353 15188 2.092882 GTAGTGCGACGGCCACTTC 61.093 63.158 16.13 8.80 38.85 3.01
1446 15281 2.685380 AGGAACCTGGAGCCCTCG 60.685 66.667 0.00 0.00 0.00 4.63
1502 15337 3.197790 CGGACCGCTGCTTGATGG 61.198 66.667 0.00 0.00 0.00 3.51
1513 15348 1.741770 CTTCCTCTTTGGCGGACCG 60.742 63.158 10.29 10.29 39.70 4.79
1514 15355 0.391793 CTCTTCCTCTTTGGCGGACC 60.392 60.000 0.00 0.00 35.26 4.46
1517 15358 0.391793 GTCCTCTTCCTCTTTGGCGG 60.392 60.000 0.00 0.00 35.26 6.13
1518 15359 0.737715 CGTCCTCTTCCTCTTTGGCG 60.738 60.000 0.00 0.00 35.26 5.69
1523 15364 1.939769 GCTCGCGTCCTCTTCCTCTT 61.940 60.000 5.77 0.00 0.00 2.85
1524 15365 2.411504 GCTCGCGTCCTCTTCCTCT 61.412 63.158 5.77 0.00 0.00 3.69
1525 15366 2.103340 GCTCGCGTCCTCTTCCTC 59.897 66.667 5.77 0.00 0.00 3.71
1617 15477 0.680618 CCCAACATGCAAGAGCCAAA 59.319 50.000 0.00 0.00 41.13 3.28
1690 15550 8.090250 TGGTACACATGAAACAAGTAATACAC 57.910 34.615 0.00 0.00 0.00 2.90
1691 15551 7.934665 ACTGGTACACATGAAACAAGTAATACA 59.065 33.333 0.00 0.00 0.00 2.29
1710 18074 2.825861 TTTCTCCGGAACACTGGTAC 57.174 50.000 5.23 0.00 0.00 3.34
1715 18079 4.764823 TGCAATATTTTTCTCCGGAACACT 59.235 37.500 5.23 0.00 0.00 3.55
1721 18085 5.215160 GCATACTGCAATATTTTTCTCCGG 58.785 41.667 0.00 0.00 44.26 5.14
1779 18167 8.622157 GGGTTTGCTTCCTTACTCTATTTAATC 58.378 37.037 0.00 0.00 0.00 1.75
1788 18176 1.813178 GCTGGGTTTGCTTCCTTACTC 59.187 52.381 0.00 0.00 0.00 2.59
1789 18177 1.547901 GGCTGGGTTTGCTTCCTTACT 60.548 52.381 0.00 0.00 0.00 2.24
1794 18182 0.540597 AAGAGGCTGGGTTTGCTTCC 60.541 55.000 0.00 0.00 37.26 3.46
1798 18186 1.271379 TGACTAAGAGGCTGGGTTTGC 60.271 52.381 0.00 0.00 0.00 3.68
1799 18187 2.039084 AGTGACTAAGAGGCTGGGTTTG 59.961 50.000 0.00 0.00 0.00 2.93
1802 18190 1.625818 CAAGTGACTAAGAGGCTGGGT 59.374 52.381 0.00 0.00 0.00 4.51
1804 18192 1.625818 ACCAAGTGACTAAGAGGCTGG 59.374 52.381 0.00 0.00 0.00 4.85
1807 18195 1.404315 CGGACCAAGTGACTAAGAGGC 60.404 57.143 0.00 0.00 0.00 4.70
1808 18196 2.094649 GTCGGACCAAGTGACTAAGAGG 60.095 54.545 0.00 0.00 0.00 3.69
1810 18198 1.891150 GGTCGGACCAAGTGACTAAGA 59.109 52.381 22.10 0.00 38.42 2.10
1811 18199 2.365408 GGTCGGACCAAGTGACTAAG 57.635 55.000 22.10 0.00 38.42 2.18
1823 18211 2.140717 CTTGTAAACCACTGGTCGGAC 58.859 52.381 0.00 0.00 33.12 4.79
1824 18212 2.040939 TCTTGTAAACCACTGGTCGGA 58.959 47.619 0.00 0.00 33.12 4.55
1825 18213 2.536761 TCTTGTAAACCACTGGTCGG 57.463 50.000 0.00 0.00 33.12 4.79
1826 18214 4.886247 TTTTCTTGTAAACCACTGGTCG 57.114 40.909 0.00 0.00 33.12 4.79
1827 18215 5.358725 TCCTTTTTCTTGTAAACCACTGGTC 59.641 40.000 0.00 0.00 33.12 4.02
1828 18216 5.126545 GTCCTTTTTCTTGTAAACCACTGGT 59.873 40.000 0.00 0.00 37.65 4.00
1829 18217 5.451381 GGTCCTTTTTCTTGTAAACCACTGG 60.451 44.000 0.00 0.00 0.00 4.00
1830 18218 5.451381 GGGTCCTTTTTCTTGTAAACCACTG 60.451 44.000 0.00 0.00 0.00 3.66
1831 18219 4.647853 GGGTCCTTTTTCTTGTAAACCACT 59.352 41.667 0.00 0.00 0.00 4.00
1832 18220 4.202182 GGGGTCCTTTTTCTTGTAAACCAC 60.202 45.833 0.00 0.00 0.00 4.16
1833 18221 3.962063 GGGGTCCTTTTTCTTGTAAACCA 59.038 43.478 0.00 0.00 0.00 3.67
1834 18222 4.220724 AGGGGTCCTTTTTCTTGTAAACC 58.779 43.478 0.00 0.00 0.00 3.27
1835 18223 5.597182 AGAAGGGGTCCTTTTTCTTGTAAAC 59.403 40.000 0.34 0.00 44.82 2.01
1836 18224 5.773091 AGAAGGGGTCCTTTTTCTTGTAAA 58.227 37.500 0.34 0.00 44.82 2.01
1837 18225 5.397553 AGAAGGGGTCCTTTTTCTTGTAA 57.602 39.130 0.34 0.00 44.82 2.41
1838 18226 5.397553 AAGAAGGGGTCCTTTTTCTTGTA 57.602 39.130 12.14 0.00 44.82 2.41
1839 18227 3.973472 AGAAGGGGTCCTTTTTCTTGT 57.027 42.857 0.34 0.00 44.82 3.16
1841 18229 5.487488 ACAAAAAGAAGGGGTCCTTTTTCTT 59.513 36.000 9.14 8.88 44.82 2.52
1842 18230 5.030147 ACAAAAAGAAGGGGTCCTTTTTCT 58.970 37.500 9.14 0.00 44.82 2.52
1843 18231 5.116180 CACAAAAAGAAGGGGTCCTTTTTC 58.884 41.667 9.14 0.00 44.82 2.29
1844 18232 4.080582 CCACAAAAAGAAGGGGTCCTTTTT 60.081 41.667 0.00 0.00 44.82 1.94
1845 18233 3.454447 CCACAAAAAGAAGGGGTCCTTTT 59.546 43.478 0.34 0.00 44.82 2.27
1846 18234 3.038280 CCACAAAAAGAAGGGGTCCTTT 58.962 45.455 0.34 0.00 44.82 3.11
1848 18236 1.757764 GCCACAAAAAGAAGGGGTCCT 60.758 52.381 0.00 0.00 33.87 3.85
1849 18237 0.679505 GCCACAAAAAGAAGGGGTCC 59.320 55.000 0.00 0.00 0.00 4.46
1851 18239 0.031616 TGGCCACAAAAAGAAGGGGT 60.032 50.000 0.00 0.00 0.00 4.95
1852 18240 0.681175 CTGGCCACAAAAAGAAGGGG 59.319 55.000 0.00 0.00 0.00 4.79
1855 18243 0.318955 CGCCTGGCCACAAAAAGAAG 60.319 55.000 14.12 0.00 0.00 2.85
1856 18244 1.739049 CGCCTGGCCACAAAAAGAA 59.261 52.632 14.12 0.00 0.00 2.52
1857 18245 2.855514 GCGCCTGGCCACAAAAAGA 61.856 57.895 14.12 0.00 34.80 2.52
1859 18247 4.277593 CGCGCCTGGCCACAAAAA 62.278 61.111 14.12 0.00 38.94 1.94
1881 18422 0.463833 CTTTGTAGGGGTGCCGGATC 60.464 60.000 5.05 0.00 0.00 3.36
1886 18427 2.812358 CAAAACTTTGTAGGGGTGCC 57.188 50.000 0.00 0.00 33.59 5.01
1927 18468 6.092259 GCTAGGCGACAGATCTTTTAAAAAGA 59.908 38.462 1.66 0.00 0.00 2.52
1928 18469 6.251549 GCTAGGCGACAGATCTTTTAAAAAG 58.748 40.000 1.66 0.00 0.00 2.27
1929 18470 6.178239 GCTAGGCGACAGATCTTTTAAAAA 57.822 37.500 1.66 0.00 0.00 1.94
1930 18471 5.796350 GCTAGGCGACAGATCTTTTAAAA 57.204 39.130 0.00 0.00 0.00 1.52
1949 18490 1.132453 CACCAGATCAACGACTCGCTA 59.868 52.381 0.00 0.00 0.00 4.26
1960 18501 1.407851 GGCTGCTCAATCACCAGATCA 60.408 52.381 0.00 0.00 31.90 2.92
1967 18509 1.751927 CCCCAGGCTGCTCAATCAC 60.752 63.158 9.56 0.00 0.00 3.06
1968 18510 2.202236 GACCCCAGGCTGCTCAATCA 62.202 60.000 9.56 0.00 0.00 2.57
1969 18511 1.452833 GACCCCAGGCTGCTCAATC 60.453 63.158 9.56 0.00 0.00 2.67
1970 18512 2.233566 TGACCCCAGGCTGCTCAAT 61.234 57.895 9.56 0.00 0.00 2.57
1977 18519 2.936032 GGAAGGTGACCCCAGGCT 60.936 66.667 0.00 0.00 34.66 4.58
1978 18520 2.558380 GATGGAAGGTGACCCCAGGC 62.558 65.000 5.83 0.00 37.06 4.85
1981 18523 1.005805 CAATGATGGAAGGTGACCCCA 59.994 52.381 0.00 0.00 37.86 4.96
1996 18538 0.998669 CGCGACATGTGTAGCAATGA 59.001 50.000 16.43 0.00 45.11 2.57
2014 18556 5.858159 TGTTACAGAAAATTTTCGCAACG 57.142 34.783 21.98 13.12 41.92 4.10
2087 18659 4.737765 CCACAACAAAACATCCGTTACAAG 59.262 41.667 0.00 0.00 33.99 3.16
2211 18909 1.264288 CGAGTTTCTGCAACAAGGTCC 59.736 52.381 0.00 0.00 37.93 4.46
2281 18991 2.998480 ATACACCGTCGCCCACCA 60.998 61.111 0.00 0.00 0.00 4.17
2345 19206 0.698238 TAAACTCATGCTGCACCCCT 59.302 50.000 3.57 0.00 0.00 4.79
2349 19210 1.135575 GTGCCTAAACTCATGCTGCAC 60.136 52.381 3.57 0.00 40.49 4.57
2450 19342 2.273179 ACTACTTCGACAGCGGCCA 61.273 57.895 2.24 0.00 38.28 5.36
2453 19345 2.152699 CGCACTACTTCGACAGCGG 61.153 63.158 0.00 0.00 41.30 5.52
2454 19346 1.128724 CTCGCACTACTTCGACAGCG 61.129 60.000 0.00 0.00 45.79 5.18
2457 19349 1.199327 CCTTCTCGCACTACTTCGACA 59.801 52.381 0.00 0.00 0.00 4.35
2514 19406 2.513204 CCCACGAGAGCAGCCATG 60.513 66.667 0.00 0.00 0.00 3.66
2515 19407 3.790437 CCCCACGAGAGCAGCCAT 61.790 66.667 0.00 0.00 0.00 4.40
2541 19433 1.138859 CTGGTATGTTGCGGGATCTGA 59.861 52.381 0.00 0.00 0.00 3.27


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.